Exploration of the persistent components obtained from the deconvolution of gene expression PBMC dataset
Context: Comparison between CoGAPS and sICA
12/22/21
1 Introduction
Here we perform the annotation of the persistent components extracted from the single cell RNASeq dataset of PBMC (GSE132044). On this dataset, we used only 10x v2 data.
2 Description of the persistent components
2.1 Top-contributing genes
The top-contributing genes are shown below for each persistent component. Top-contributing genes of a persistent component are the genes whose weights are below or beyond 3 sd from the mean of the weigths in this persistent component.
## [1] TRUE3 Annotation of the persistent components using gene sets of immune cell types
We used only MCPcounter gene sets and checked if the persistent components were enriched in these gene sets.
For that, we performed over representation analysis of the top-contributing genes of the positive and negative tails of each persistent component using immunce cell types gene sets.
3.1 MCPcounter
For each persistent component, a total of 10 gene sets are tested.
There are a total of 8 significant enrichments in positive tails and 4 significant enrichment in negative tails.
There are 5 unique MCPcounter cell types with significant enrichments in the top contributing genes of the positive tails and 3 unique MCPcounter cell types with significant enrichments in their targers in the top_contributing genes of the negative tails.
4 Annotation of the persistent components using GO, KEGG, MSigDB and DO
To decipher the mechnanisms active in the persistent components, we extracted the top_contributing genes in each persistent component and performed over representation analysis as well as gene set enrichment analyses on each persistent component.
4.1 Over representation analysis of the top contributing genes and gene set enrichment analysis for each persistent component
Now we can describe each component in details. We used GO, KEGG, MSigDB (http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp) and DO ontology to annotate the persistent components. Results are represented in dotplots, cnetplots and emaplots for both drivers of the positive and negative tails using clusterProfiler (https://bookdown.org/yihui/rmarkdown/html-document.html). If the OR analysis had no enrichment in one or the two tails, no plot is reported.
4.1.1 Persistent component 1
4.1.1.1 GO enrichment for persistent component 1
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.1.2 KEGG enrichment for persistent component 1
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.1.3 MSigDB enrichment for persistent component 1
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.1.4 DO enrichment for persistent component 1
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.2 Persistent component 2
4.1.2.1 GO enrichment for persistent component 2
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.2.2 KEGG enrichment for persistent component 2
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.2.3 MSigDB enrichment for persistent component 2
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.2.4 DO enrichment for persistent component 2
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.3 Persistent component 3
4.1.3.1 GO enrichment for persistent component 3
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.3.2 KEGG enrichment for persistent component 3
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.3.3 MSigDB enrichment for persistent component 3
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.3.4 DO enrichment for persistent component 3
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.4 Persistent component 4
4.1.4.1 GO enrichment for persistent component 4
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.4.2 KEGG enrichment for persistent component 4
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.4.3 MSigDB enrichment for persistent component 4
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.4.4 DO enrichment for persistent component 4
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.5 Persistent component 5
4.1.5.1 GO enrichment for persistent component 5
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.5.2 KEGG enrichment for persistent component 5
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.5.3 MSigDB enrichment for persistent component 5
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.5.4 DO enrichment for persistent component 5
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.6 Persistent component 6
4.1.6.1 GO enrichment for persistent component 6
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.6.2 KEGG enrichment for persistent component 6
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.6.3 MSigDB enrichment for persistent component 6
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.6.4 DO enrichment for persistent component 6
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.7 Persistent component 7
4.1.7.1 GO enrichment for persistent component 7
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.7.2 KEGG enrichment for persistent component 7
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.7.3 MSigDB enrichment for persistent component 7
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.7.4 DO enrichment for persistent component 7
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.8 Persistent component 8
4.1.8.1 GO enrichment for persistent component 8
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.8.2 KEGG enrichment for persistent component 8
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.8.3 MSigDB enrichment for persistent component 8
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.8.4 DO enrichment for persistent component 8
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.9 Persistent component 9
4.1.9.1 GO enrichment for persistent component 9
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.9.2 KEGG enrichment for persistent component 9
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.9.3 MSigDB enrichment for persistent component 9
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.9.4 DO enrichment for persistent component 9
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.10 Persistent component 10
4.1.10.1 GO enrichment for persistent component 10
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.10.2 KEGG enrichment for persistent component 10
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.10.3 MSigDB enrichment for persistent component 10
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.10.4 DO enrichment for persistent component 10
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.11 Persistent component 11
4.1.11.1 GO enrichment for persistent component 11
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.11.2 KEGG enrichment for persistent component 11
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.11.3 MSigDB enrichment for persistent component 11
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.11.4 DO enrichment for persistent component 11
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.12 Persistent component 12
4.1.12.1 GO enrichment for persistent component 12
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.12.2 KEGG enrichment for persistent component 12
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.12.3 MSigDB enrichment for persistent component 12
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.12.4 DO enrichment for persistent component 12
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.13 Persistent component 13
4.1.13.1 GO enrichment for persistent component 13
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.13.2 KEGG enrichment for persistent component 13
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.13.3 MSigDB enrichment for persistent component 13
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.13.4 DO enrichment for persistent component 13
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.14 Persistent component 14
4.1.14.1 GO enrichment for persistent component 14
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.14.2 KEGG enrichment for persistent component 14
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.14.3 MSigDB enrichment for persistent component 14
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.14.4 DO enrichment for persistent component 14
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.15 Persistent component 15
4.1.15.1 GO enrichment for persistent component 15
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.15.2 KEGG enrichment for persistent component 15
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.15.3 MSigDB enrichment for persistent component 15
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.15.4 DO enrichment for persistent component 15
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.16 Persistent component 16
4.1.16.1 GO enrichment for persistent component 16
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.16.2 KEGG enrichment for persistent component 16
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.16.3 MSigDB enrichment for persistent component 16
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.16.4 DO enrichment for persistent component 16
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.17 Persistent component 17
4.1.17.1 GO enrichment for persistent component 17
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.17.2 KEGG enrichment for persistent component 17
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.17.3 MSigDB enrichment for persistent component 17
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.17.4 DO enrichment for persistent component 17
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.18 Persistent component 18
4.1.18.1 GO enrichment for persistent component 18
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.18.2 KEGG enrichment for persistent component 18
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.18.3 MSigDB enrichment for persistent component 18
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.18.4 DO enrichment for persistent component 18
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.19 Persistent component 19
4.1.19.1 GO enrichment for persistent component 19
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.19.2 KEGG enrichment for persistent component 19
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.19.3 MSigDB enrichment for persistent component 19
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.19.4 DO enrichment for persistent component 19
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.20 Persistent component 20
4.1.20.1 GO enrichment for persistent component 20
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.20.2 KEGG enrichment for persistent component 20
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.20.3 MSigDB enrichment for persistent component 20
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.20.4 DO enrichment for persistent component 20
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.21 Persistent component 21
4.1.21.1 GO enrichment for persistent component 21
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.21.2 KEGG enrichment for persistent component 21
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.21.3 MSigDB enrichment for persistent component 21
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.21.4 DO enrichment for persistent component 21
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.22 Persistent component 22
4.1.22.1 GO enrichment for persistent component 22
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.22.2 KEGG enrichment for persistent component 22
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.22.3 MSigDB enrichment for persistent component 22
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.22.4 DO enrichment for persistent component 22
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.23 Persistent component 23
4.1.23.1 GO enrichment for persistent component 23
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.23.2 KEGG enrichment for persistent component 23
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.23.3 MSigDB enrichment for persistent component 23
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.23.4 DO enrichment for persistent component 23
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.24 Persistent component 24
4.1.24.1 GO enrichment for persistent component 24
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.24.2 KEGG enrichment for persistent component 24
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.24.3 MSigDB enrichment for persistent component 24
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.24.4 DO enrichment for persistent component 24
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.25 Persistent component 25
4.1.25.1 GO enrichment for persistent component 25
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.25.2 KEGG enrichment for persistent component 25
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.25.3 MSigDB enrichment for persistent component 25
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.25.4 DO enrichment for persistent component 25
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.26 Persistent component 26
4.1.26.1 GO enrichment for persistent component 26
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.26.2 KEGG enrichment for persistent component 26
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.26.3 MSigDB enrichment for persistent component 26
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.26.4 DO enrichment for persistent component 26
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.27 Persistent component 27
4.1.27.1 GO enrichment for persistent component 27
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.27.2 KEGG enrichment for persistent component 27
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.27.3 MSigDB enrichment for persistent component 27
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.27.4 DO enrichment for persistent component 27
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.28 Persistent component 28
4.1.28.1 GO enrichment for persistent component 28
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.28.2 KEGG enrichment for persistent component 28
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.28.3 MSigDB enrichment for persistent component 28
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.28.4 DO enrichment for persistent component 28
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.29 Persistent component 29
4.1.29.1 GO enrichment for persistent component 29
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.29.2 KEGG enrichment for persistent component 29
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.29.3 MSigDB enrichment for persistent component 29
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.29.4 DO enrichment for persistent component 29
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.1.30 Persistent component 30
4.1.30.1 GO enrichment for persistent component 30
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
4.1.30.2 KEGG enrichment for persistent component 30
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
4.1.30.3 MSigDB enrichment for persistent component 30
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
4.1.30.4 DO enrichment for persistent component 30
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
4.2 Overview of over representation analysis in top_contributing genes of all persistent components
Top_contributing genes were submitted to over representation analysis. First, we show an overview of the top_contributing genes coming from the postive and negative tails for all components and next, we give details about each component.
5 Annotation of the persistent components using gene sets of transcription factors
We used Dorothea database (Discriminant Regulon Expression Analysis, https://saezlab.github.io/dorothea/, Garcia-Alonso L et al. 2019) to construct gene sets of each of the reported transcription factor. We then checked if the persistent components were enriched in some of these TF gene sets.
For that, we performed over representation analysis of the top-contributing genes of the positive and negative tails of each persistent component using the TF gene sets.
For each persistent component, a total of 361 gene sets are tested.
There are a total of 14 significant enrichments in positive tails and 9 significant enrichment in negative tails.
There are 12 unique TFs with significant enrichments in their targets in the top_contributing genes of the positive tails and 9 unique TFs with significant enrichments in their targets in the top_contributing genes of the negative tails.